28 December 2011

If last year could be seen as a breakout year for Marmorkrebs research, this one might be counted as a correction.

As anyone who’s studied statistics should know, an extraordinary event is more likely to be followed by a rather more ordinary one. I am hoping this is just a temporary dip for Marmorkrebs research, and that in 2012, the upward trend will resume. And on a personal note, I look forward to carrying out the research funded by #SciFund in 2012!

In the larger crustacean realm, probably one of the most noteworthy news stories of the year was the publication of the first crustacean genome. But I keep wondering every time I hear about the advances of high throughput sequencing and how cheap and easy it’s getting... why don’t I have a crayfish genome yet? Grumble grumble grumble.

20 December 2011

I got the hardcopy of the newest issue of Freshwater Crayfish last week. It’s the first part of volume 18. The production values are good, with sharp figure reproductions and gloss paper. There are some colour figures, too!

As I mentioned previously, the society International Association of Astacology really wants to have a push to get the journal published much more regularly. It used to be published only in alternate years. The society hopes that this will allow Freshwater Crayfish to be indexed in services like ISI Web of Science, which would mean that the journal could get an official Impact Factor.

Manuscripts for Freshwater Crayfish are now being accepted continually. The turnaround time from submission to publication should be on the order of months, rather than years. Submissions can uploaded to: http://iz.carnegiemnh.org/FCEditor/

Disclosure: I have an article in this issue, though not on Marmorkrebs.

Phosphatized globular microfossils from the Ediacaran and Lower Cambrian of South China represent an impressive record of early animal evolution and development, however their affinity based on putative embryonic metazoan, bacterial and inorganic features is strongly debated. Understanding key processes and conditions that cause exceptional egg and embryo preservation and fossilization are therefore crucial for a reliable interpretation of their phylogenetic position. Taphonomic experiments on eggs of the marbled crayfish indicate a close link between early mineralization and rapid anaerobic decay of the endochorional envelope, producing different preservational stages of degradation resembling the various decay stages observed in the fossil record. Stabilization of the spherical morphology was achieved by pre-heating of the eggs. Complete surface mineralization occurred under reduced conditions within one to two weeks, with fine-grained brushite (CaHPO4·2H2O) over calcite as the dominating mineral phase. Although the endochorional envelope was not preserved, experiments resulted in exceptional preservation of the embryonic tissue at the cellular level. Thus our findings suggest that the mechanisms of decay, preservation of surface structures, and mineral replacement in the experiment and during fossilization of Cambrian embryos were likely operating at a similar rationale.

Keywords: None provided.

Note: This discussion paper is under review for the journal Biogeosciences. This journal has an editorial policy that differs from many other journals, described as “innovative two-stage publication process with Public Peer-Review & Interactive Public Discussion.” The paper is initially published – permanently archived – in Biogeosciences Discussions, to receive comments (which are also archived). If the paper is accepted by the editors of Biogeosciences, the final version appears in that journal as the “copy of record.” If not, the paper remains in Biogeosciences Discussions, does not contribute to the Biogeosciences’ Impact Factor, etc.

15 December 2011

And there’s the siren! The #SciFund challenge has came to an end! Here are some of my initial reactions to the experience.

Things that I didn’t expect:

Fewer people, bigger donations. I thought most donations would be small – a dollar or two – and projects would have hundreds of supporters. Instead, projects had tens of supporters contributing $10-20, and more, often much more. Consequently, my “I make my target if everyone chips in 50 cents” pitch to my several thousand followers on Twitter and Google Plus wasn’t effective.

Cool beats practical: Given how much talk there is on how people want to see “results” and “return on investment” in traditional funding, my one post where I described how my research might have a practical pay-off to aquaculture got the least hits of anything I did to promote my project over six weeks.

Weak relationship between video views and dollars. “Duck force” got more than ten times the views of my video, but it didn’t get ten times the donations.

Front end loaded: I expected most funds to come in at the very beginning and the very end. RocketHub confirmed that this is the normal pattern. But the “bump” in the last few days was much smaller than I expected. On my project, the amount of dollars raised and time elapsed were pretty tightly correlated.

So emotional: I touched on this before here. I got way more wrapped up in this tiny little fundraising effort than most other projects.

Not much variation. Most projects raised about the same amount, regardless of their targets. $1,000 or so seems to be the sweet spot for now.

I made the right call to keep my project target small. At one point, I almost raised it, and if I had, I don’t think I would have made it. Projects that want to raise ten grand are either going to have to be brilliant or wait for the crowdfunding of science to mature.

Things that disappointed me:

Notice us! We didn’t get as much attention from science media as I expected. No coverage in the Science, Nature, The Guardian, The New York Times, Quirks and Quarks, and so on.

Whiff: Thirty-nine projects didn’t meet their targets.

Low gear: I was hoping to be one of the first projects to get past the post. I though that I would have a good shot at it, based on responses of people to whom I showed my video, and that I had one of the lowest targets.

Left undone: I had ideas for three more videos that I didn’t get to make.

Things that made me happy:

Mad skills: I learned a lot about how to make short videos. I may be doing more.

10 December 2011

I was sitting at home, working on just one last video to try to convince people to support my #SciFund project, when I heard the sound of an email alert. When I saw it was from RocketHub, I was excited, because I had been getting close to my target. How much closer might I get?

When I read the email, I almost had a heart attack. It was enough to push me past the finish line!

My day went from this:

To this:

(Since I was sitting at a computer, of course my first move was to tweet about it.)

The #SciFund challenge isn’t over! I still want to see if I can squeeze out one more video promoting my project. We are allowed to have donations exceed the target. If there is enough money, I will take a student with me on the expedition! And RocketHub even rewards people who fuel a project after it hits its target with the Supernova badge!

And for those who watched my promo video all the way to the end, you’ll know I have another project I promised to reveal if I met my target:

The Beach of the Goliath Crabs!

I will be revealing the secret of this project soon!

Thank you to those who have supported this project, either financially or morally!

For comprehensive study of decapod phylogeny on mitochondrial genome level, we completely sequenced 13 decapods. Together with available 32 decapods from GenBank, the datasets now covered all major decapod taxa. From the sequence aspect, Maximum likelihood (ML) and Bayesian inference (BI) of nucleotide, genome and amino acid datasets revealed similar topologies at the higher level relationships: Brachyura,Anomala), Thalassinida), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Only Polychelida received two different positions: the basal branch of Reptantia in ML analysis of amino acid data and the sister group of Astacidea in the resting analyses. On the family level, Thalassinida is paraphyletic, which is consistent with some morphological and some recent molecular results (e.g. de Saint Laurent 1973, Tsang et al. 2008), other taxa are monophyletic. These major results confirm some of the traditional morphological views. In the gene arrangements aspect, two notable features in astacid mitogenomes evolution have been observed: a huge inversion happened in Procambarus fallax f. virginalis, Homarus gammarus and one priapulid Priapulus caudatus is supposed to be of convergent nature within the Ecdysozoa; complete loss of protein coding gene nad2 in H. gammarus and partial loss in Enoplometopus occidentalis are supposed to be synapomorphic character for Nephropidae. Additionally, a new gene rearrangement model – “invertion triggered duplication” model is also proposed according to decapod gene rearrangements. Anyhow, the mitogenomes show a good potential to resolve the relationship within Decapoda.